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Merge pull request #1613 from lindenb/pl_goleft #6940

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Merge pull request #1613 from lindenb/pl_goleft

Merge pull request #1613 from lindenb/pl_goleft #6940

GitHub Actions / JUnit Test Report failed Dec 10, 2024 in 0s

9 tests run, 8 passed, 0 skipped, 1 failed.

Annotations

Check failure on line 1 in Test pipeline

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline.Run with profile test | --aligner bwa-mem --save_reference | skip QC/recal/md 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.11.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [sick_almeida] DSL2 - revision: 3954909713
Downloading plugin [email protected]
Downloading plugin [email protected]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek 3.5.0
------------------------------------------------------
Input/output options
  input                     : /home/runner/work/sarek/sarek/tests/csv/3.0/fastq_single.csv
  outdir                    : /home/runner/work/sarek/sarek/~/tests/32e6f6b6bf722dda084f4a86b2ca64ba/output

Main options
  split_fastq               : 0
  intervals                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.interval_list
  skip_tools                : baserecalibrator,fastqc,markduplicates,mosdepth,multiqc,samtools

Annotation
  bcftools_annotations      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz
  bcftools_annotations_tbi  : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi
  bcftools_header_lines     : /home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt

General reference genome options
  igenomes_base             : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/
  save_reference            : true

Reference genome options
  genome                    : testdata.nf-core.sarek
  dbsnp                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi
  dbsnp_vqsr                : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
  dict                      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.fasta
  fasta_fai                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.fasta.fai
  germline_resource         : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz
  germline_resource_tbi     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi
  known_indels              : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
  known_indels_tbi          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi
  known_indels_vqsr         : --resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz
  ngscheckmate_bed          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed
  sentieon_dnascope_model   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
  snpeff_cache              : null
  snpeff_db                 : WBcel235.105
  vep_cache                 : null
  vep_cache_version         : 113
  vep_genome                : WBcel235
  vep_species               : caenorhabditis_elegans

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
  modules_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Core Nextflow options
  runName                   : sick_almeida
  containerEngine           : singularity
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/32e6f6b6bf722dda084f4a86b2ca64ba
  workDir                   : /home/runner/work/sarek/sarek/~/tests/32e6f6b6bf722dda084f4a86b2ca64ba/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,singularity
  configFiles               : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.12688/f1000research.16665.2
    https://doi.org/10.1093/nargab/lqae031
    https://doi.org/10.5281/zenodo.3476425

* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/sarek/blob/master/CITATIONS.md

Downloading plugin [email protected]
WARN: FASTQ file(/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz): Cannot extract flowcell ID from @normal#21#998579#1/1
WARN: FASTQ file(/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz): Cannot extract flowcell ID from @normal#21#998579#1/1
Pulling Singularity image https://depot.galaxyproject.org/singularity/bwa:0.7.18--he4a0461_0 [cache /home/runner/work/sarek/sarek/.singularity/depot.galaxyproject.org-singularity-bwa-0.7.18--he4a0461_0.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0 [cache /home/runner/work/sarek/sarek/.singularity/depot.galaxyproject.org-singularity-gatk4-4.5.0.0--py36hdfd78af_0.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/gawk:5.1.0 [cache /home/runner/work/sarek/sarek/.singularity/depot.galaxyproject.org-singularity-gawk-5.1.0.img]
[5f/0127bc] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (genome.interval_list)
Pulling Singularity image https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2 [cache /home/runner/work/sarek/sarek/.singularity/depot.galaxyproject.org-singularity-htslib-1.20--h5efdd21_2.img]
[6e/2c211c] Submitted process > NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX (genome.fasta)
Pulling Singularity image https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0 [cache /home/runner/work/sarek/sarek/.singularity/depot.galaxyproject.org-singularity-mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40-1bd8542a8a0b42e0981337910954371d0230828e-0.img]
[da/aaf8f5] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr22_1-40001)
[b8/5ffa3a] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test-test_L1)
[ec/fdbd40] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test-test_L2)
Pulling Singularity image https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0 [cache /home/runner/work/sarek/sarek/.singularity/depot.galaxyproject.org-singularity-samtools-1.21--h50ea8bc_0.img]
[a7/ecd74e] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (test)
[34/bd572f] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (test)
[b5/c32ce9] Submitted process > NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING (test)
ERROR ~ Error executing process > 'NFCORE_SAREK:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED (1)'

Caused by:
  Failed to pull singularity image
    command: singularity pull  --name depot.galaxyproject.org-singularity-gatk4-4.5.0.0--py36hdfd78af_0.img.pulling.1733838895569 https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0 > /dev/null
    status : 143
    hint   : Try and increase singularity.pullTimeout in the config (current is "20m")
    message:
      INFO:    Downloading network image



 -- Check '/home/runner/work/sarek/sarek/~/tests/32e6f6b6bf722dda084f4a86b2ca64ba/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/sarek/sarek/~/tests/32e6f6b6bf722dda084f4a86b2ca64ba/meta/nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-
Nextflow stderr:
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